Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= reanno::Pedo557:CA265_RS14455 (443 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 154 bits (389), Expect = 5e-42 Identities = 128/426 (30%), Positives = 203/426 (47%), Gaps = 75/426 (17%) Query: 28 YDME--KSHGAYIYDAKHNRTLLDFFTCFASVPLGYNHP---KMINDEAFKKNLFLAALA 82 YD+ K G ++D ++ LD + A + +G+ HP +MI+++ +A L Sbjct: 10 YDINIVKGQGCKVWD-ENGTEYLDLYGGHAVISIGHAHPHYVEMISNQ-------VATLG 61 Query: 83 NPSNSDVYTQQYAQFVETFSKV-GIPDYLPHAFFIAGGGLAVENAIKVAMDWKVQKNFAK 141 SNS V + Q E K+ G DY F I G A ENA+K+A +F Sbjct: 62 FYSNS-VINKLQQQVAERLGKISGYEDY--SLFLINSGAEANENALKLA-------SFYN 111 Query: 142 GYTEEKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFAKFDWPRVAVPEVKFPLSGNNL 201 G T KV+ F +AFHGRT + TN P + P+ NN Sbjct: 112 GRT-----KVISFSKAFHGRTSLAVEATNN------------------PTIIAPI--NNN 146 Query: 202 SHAIQTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGDNHLREEFLIQIKALADENDAF 261 H + +K+ +A K D+CA+I+E IQ GG EF+ +++ + E Sbjct: 147 GHVTYLPLNDIEAMKQELA--KGDVCAVIIEGIQGVGGIKIPTTEFMQELRKVCTETGTI 204 Query: 262 LIYDEVQTGVGLTGKFWCHQHFSEKARPDIL----AFGKKMQVCGILVGHKVDQVETNVF 317 LI DE+Q+G G +GKF+ HQ+ +PDI+ G + G+L+ + +F Sbjct: 205 LILDEIQSGYGRSGKFFAHQY--NHIQPDIITVAKGIGNGFPMAGVLI--------SPMF 254 Query: 318 K-VPSRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYLKDQLENLSHRFDQMTN 376 K V ++ +T+GGN + + ++ ++E+D L ENA VG YL ++L+ +F Q+ Sbjct: 255 KPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLEELK----KFPQIKE 310 Query: 377 VRGRGLLCSFDF--PTKEMRNTFIAKGLENNVMFLGCGEKTIRFRPALCIEQKHIDEGLT 434 VRGRGL+ +F P KE+R+ I + +V G +R P LC+ + DE L Sbjct: 311 VRGRGLMIGLEFEEPIKELRSRLI---YDEHVFTGASGTNVLRLLPPLCLSMEEADEFLA 367 Query: 435 VMDKIL 440 ++L Sbjct: 368 RFKRVL 373 Lambda K H 0.321 0.137 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 405 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 443 Length of database: 373 Length adjustment: 31 Effective length of query: 412 Effective length of database: 342 Effective search space: 140904 Effective search space used: 140904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory